It was a normal day in the life of Sakai Yūji, a 15 year-old highschool student, but then all of a sudden his life changed. When a Monster called "Guze no Tomogara" attacks him and everyone around him, turning them into blue flames and consuming them, Yūji's life gets saved by the Flame-Haired Burning-Eyed Hunter. A girl in a black coat, flaming red hair and a long sword, whom he would later name Shana. Confused and seeking answers Yūji follows the girl and finds out the harsh truth about everything around him.

The girl with flaming hair uncovers the truth about the world that Yuuji is living in. He learns that he is already dead, and is only lasting until his flame burns out. As he watch his classmate's flame about to burn out, Yuuji felt useless for doing nothing and wants to help. He tries his best in making an effort of giving her a good time before she leaves...

Yuuji gave the "Flaming-hair" girl a name, and that name is "Shana". The next day, Yuuji went to school looking all depressed. He heard his friend talked about the girl that disappear yesterday and became excited because his friend remembers her. Everything changed when the classroom was attack by a Tomogara. Suddenly, Shana came out of nowhere. In order to save the people around him, he must sacrifice some of his torch power to turn everything back to normal. But will Yuuji do so?

Shana has come to the conclusion that Yuuji is restricting her role as a Flame Haze and is forced to make terrible decisions. Just when she is about to carry out her decision, Friagne begins to make his move on his City-Devouring plans. Can he be stopped in time?

Back before Shana became a Flame Haze, she was living in a large castle-like structure floating in the sky along with Alastor and a maid who cares for her. One day, a Denizen attacks the maid, whose name is Wilhelmina Carmel, who also happens to be a Flame Haze.

The Seeking Research Denizen has already started his plan to open up a gate to another dimension and now all three Flame Haze must work together to defeat him.

Wilhelmina arrives in Misaki and meets up with Shana again. Meanwhile, Margery Daw finally leaves Misaki without saying goodbye to either Eita or Keisaku. Also, Wilhelmina comes to the conclusion that Yuji must be destroyed in order to protect the balance of the world.

Shana is able to persuade Wilhelmina, at least for now, to not destroy Yuji, who has finally decided to leave Misaki in order to protect it. Later at the bonfire which burned much of the decorations from the festival, a spell is activated.

While fighting within the Seirei-den, a spell is cast which drains their power of existence for a time, however, Margery Daw comes back and destroys the spell. Ultimately, it is now up to Shana to decide the fate of Yuji.

After managing to defeat Hecate, the city is about to be destroyed regardless. However, there is one final plan, though Shana's life may be on the line if it succeeds.

Yuji has been put to sleep by a Denizen as he encounters events from the past in a dream. When he realize he was only dreaming, the spell was broken. He awoke to see Shana destroying the Denizen, calling it "weak". However, it was not the true form.

Yuji is placed in a dream again, along with Shana, in another plot to steal the Reiji Maigo.

A student that looks very much like Hecate has transferred into Yuji's class, Konoe Fumina. By using a Tomogara, Shana wants to make sure she if she is Hecate or not.

Ike suggested to visit the amusement park as a welcome for Konoe, but the carefully planned outting turns out all wrong when he miscalculated certain events. His underlying plan of impressing Kazumi was believed to be ruined initially, but he resorted to asking Kazumi to ride the Ferris wheel with him, which he was confident he would not get sick in. But mid way through the ride, he got sick. The ending dedicates Konoe thanking Ike for the outting. With Kazumi giving a smile to Ike, he ends off his unlucky day.

The episode starts off with Yuji being trained by Shana and Wilhelmina. Yuji managed to somehow defeat a Rinne that Wilhelmina summoned. In the background, Sato, one of Margery Daw's guides was silently observing, after which Sato returns and tried to plead with Margery Daw to be requested to be trained. However Margery Daw declines and subsequently tells Sato and Tanaka about her past. In her past, there appears a boy as a flame haze and the story subsequently plot around the boy and Margery Daw. The Boy is revealed to be named Yuri Chvojka.

Yuji is training with Shana in order to learn how to cast a Fuzetsu. The story shifts back to Margery's past, where she approaches to take down the two Tomogara, one of which called Anabel lures her into a trap where the stronger Tomogara manages to inflict a fatal wound on her. Just as they are about to kill Margery, Yuri comes to attack, managing to save Margery. However, Yuri becomes fatally wounded and dies in battle, ending it in a draw. The story shifts back to Yuji's training where he succeeds in casting a Fuzetsu, however, the flame of the Fuzetsu is silver. Shana and Alastor are surprised when they see the flame. Coincidentally, Margery's long hated enemy also had a silver flame.

A Fuzetsu was uncontrollably set up by Yuji, causing Margery to go berserk upon seeing the colour of the flame. Wilhelmina attempts to control the Interpreter of Condolence while Shana prevents Pheles from taking the Reiji Maigo out of Yuji. Margery attempts to attack the source of the silver flame in her blind rage, but Yuji was protected by his anti-flame ring and Pheles, who was weakening significantly, with Shana and Wilhelmina working together to restrain both. After Satou and Tanaka plead with Margery to listen to an explanation, Margery realises her folly and calms down, but only to question Yuji about what he is. Pheles then explains that the Reiji Maigo isn't what it was meant to be, and requests The Interpreter of Condolence to check the Reiji Maigo. Margery then restores everything back to normal with the help of Wilhelmina's ribbons and Yuji's Power of Existence.

The Silver awakens within Yuji due to Pheles's second attempt to free Johan. Hecate's secret is finally revealed and so she joins together with Fecor the fight.

Yuji continues his training as if he was possessed by something. Shana is concerned about Yuji's sudden change. Also a Tomogara called Zarovee appears in Misaki City.

Yuji is confused by Shana and Kazumi's words. While thinking about their words, he is ambushed by a cloning Tomogara who has a secret plan Yuji must uncover. Yuji eventually uncovers the plan, and with the help of Tanaka, is able to inform the Flame Hazes. He dispatches all of the cloned Tomogara, while Shana and Wilhelmina defeat the hidden Watcher Tomogara. Just as they kill the Tomogara, a new flame appears in the recesses of the ruins induced in the fight.

Yuji's Reiji Maigo had been taken out by Hecate who suddenly unexpected appeared alone. Bal Masqué's secret weapon, Taimei Shihen, finally starts to move.

The Statue of Pride is about to be born. When Yuji picks his sword up, he screams the name that he desires to protect, and that is Shana. After a fierce battle with the members of Bal Masqué, Shana is eventually able to break through and enter the Statue of Pride. She meets up with Yuji, and they run to fight the Tomogara with the Silver Flame at the heart of the Statue of Pride. Shana and Yuji fight together and eventually manage to beat the Tomogara, and Yuji regains the Reiji Maigo. With the heart destroyed, the Statue of Pride collapses, and Bal Masqué retreats. In the end, Yuji picks Shana over Kazumi Yoshida.

While Yuji and Shana rummage through Friagne's old pile of Treasure Tools during a hot summer's day, Yuji finds and uses a telescope-like object, causing him and Shana to switch bodies. Alastor tells the two that the object Yuji has just used is called the Reshuffle. While reversing its effect is just as easy as activating it, the Reshuffle gets lost in junk and the two have to gather the pile and find a better, isolated spot to search for the Reshuffle.

Recently, Shana has been acting strangely. Worried over her well-being, Yuji and Wilhelmina decide to follow her from the shadows after school one day.

In her early days as a Flame Haze, Shana takes over the identity of a Torch named Junko Ōgami and starts to hunt down the Denizen who killed her. She gets to know who Junko was through the latter's parents.

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Yuji's existence has disappeared on Christmas Eve after the events of Statue of Pride. Like a disappearance of a torch, all those who aren't engaged in the World of Guze have forgotten him including his closest friends and families. Shana and Kazumi still believe that Yuji exists due to the fact that their letters given to Yuji haven't disappeared. However it is shown that Yuji still exists but makes a contract with a Guze no Tomogara and takes the Serei-dens throne as the new leader of Bal Masque.

Yuji and Shana finally meet as Margery and Wilhelmina come to see what is happening. Yuji reveals that he is indeed himself but also The Snake of Festival and that he has come to save Shana from her inevitable fate as a Flame Haze—to fight against Denizens until she burns out. Shana does not believe him and the three Flame Hazes fight with Yuji. He traps Wilhelmina and Margery in a ball of silver. Yuji explains to Margery that the Silver is a projection of her emotions. He is a mirror of her hate towards everyone who abused her and has done the things Margery secretly wanted to do to them on her behalf. She has a mental breakdown and starts hysterically crying. Meanwhile, Yuji is chasing Shana and they fight. In the end, he captures her and goes to the Haridan with Shana unconscious in his arms. He takes the Haridan and claims it is his property. Yuji reveals to Yoshida, after she asks him, that he returned her letter back to let her know he chose Shana. She then falls on her knees in shock. Yuji flies to the Serei-den with Shana in his arms.

Keisaku is held hostage by an Outlaw - Widened Eye of Incineration, Emest Flieder, who believes that this way he'll make Wilhelmina join them in battle. His partner, the Scatterer of Sparkling Light, Rebecca Reed, frees Keisaku and sends him back to Margery Daw with Wilhelmina's reports. Rebecca flies to Wilhelmina, who has been her ally for a long time, and Sophie Sawallisch makes Emest the commander of the Tokyo Outlaw Headquarters. Meanwhile, at the Serei-den, Shana wonders why she couldn't do anything against Yuji and why she was so scared when he tried to catch her. She remembers when her trainer, Shiro, told her that one day she will find the greatest power that can bring down anyone and anything and then he asks to her to hold his hand. Shana then remembers how every enemy she fought, held hands with someone and she recognizes the greatest power of love that lies on the palm of Yuji's hand. Suddenly, there's a loud noise and when Shana goes out, she sees dead bodies and above them - the Master Throne, Hecate. She responds that Shana is no longer needed.

As the war continues, Shana fights her way to Nietono no Shana and is finally ready to battle.

Inside of the Divine Gate, Sabrac falls, gazing at the greatness of the Snake of the Festival in his true form. The God of Creation then sends out a signal and starts moving towards the Divine Gate. After the signal is felt by everyone, Sophie Sawallisch attempts to destroy the Gate. At the last moment Fecor protects it and dies from the power of the spell. Back in the Gate, Shana and Yuji are fighting, while Yuji now looks as he was before. Because of a memory that vows between two people are sealed with a kiss on the lips, Shana kisses Yuji on the cheek and says that is her vow. She is then taken away abruptly by the ghosts of the Flame Hazes outside of the Gate as it breaks and the Snake of the Festival comes out. All Tomogara cheer and all Flame Hazes stand in astonishment and despair and amongst this, Shana recognizes this as a sound not of a fall, but of the start of a new battle.

The Flame Haze army retreats as the Snake of the Festival destroys their morale. He announces his plan to create a new world, a complete copy of ours, to be a paradise for Tomogara and with Power of Existence flowing everywhere. Thus, all Tomogara would leave the world and the Flame Hazes would stop fighting agaist them. After that, panic and chaos reigns among the Flame Hazes, who now don't have a purpose and the Tomogara attack them.

Shana makes it to New York, and meets up with the rest of the gods of Earth. They agree to help Shana fight, and she then explains the plan to them. Yuji visited Misaki City and found Kazumi Yoshida and Eita Tanaka. He came back to convince Yoshida to join him in building the new universe. While Yoshida, Tanaka and Yuji walk around town, Yuji explains his what he intendes to do. After a while of explaining, Yoshida finally agrees to help him.

Shana reveals her plan: not to stop Yuji's goal to create a new world, but to alter the Denizens' ability to consume humans in it.

Johann and Pheles give up their existence to give way to a new form of life, they son, Justus. Many Flame Hazes also leave for the new world. Yuji intends to reverse all the damage the Denizens caused to Misaki City, including the return of Hirai, effectively undoing all the relationships that Shana has built with everyone.